I would just assume that they were just called Luke and Jake, as I know a lot more Lukes and Jakes than I do Lucases or Jacobs. In fact, despite their popularity, I don't know any Lucases and only about two Jacobs, and that's just peripherally.

I would assume that Luke was the full name and that Jake was a nn for Jacob. That is only because that has always been the case for the Lukes and Jakes that I have met. Both could be perfectly legitimate as full names and I don't think it would be that bad if people thought those were their nicknames when they first met them. That happens to my brother often, but it hasn't been an issue and people quickly learn that his name isn't short for anything.

I think Luke and Jake might be a little too close for brothers and I prefer Luke to Jake.